Substitute Abdullah El Said scored the game’s only goal a minute from time, as the Pharaohs raised their tally to four points, two shy of group leaders, Ghana who defeated Mali by a similar scoreline at the same venue. Uganda became the first team to be sent packing after conceding their second defeat of the competition.
The Cranes tried their luck through Farouk Miya five minutes later with a long shot that missed by inches as the first half ended barren.
Joseph Ochaya thought he had given Uganda an unlikely lead seven minutes after the break, but his celebrations were cut short when it was ruled offside.
Egypt coach Hector Cuper made an attacking substitution bringing on El Said for defensive midfielder Tarek Hamed. El Said made an immediate impact with his first touch but his shot on the hour mark went wide.
The Pharaohs had the last smile one minute from time. A counter attack saw substitute Mahmoud "Kahraba" Abdel Moneim passing to Salah, who laid to El Said, who drove in a shot went through the legs on Onyango to seal victory.
Total Man of the Match
Abdullah El Said (Egypt)
Hector Cuper (Head coach, Egypt)
I think all the groups are complicated not only ours. We had a difficult game against a very tough opponent. Our qualification is not guaranteed yet, so we have to fight till the end.
At the Africa Cup of Nations every match is difficult. I wished to have a bigger scoreline and better performance but I thank my players who did all their best in tough circumstances. I respect Uganda and commend them for their performance today. Every game has its own strategy and we always adjust our plans to our opponents. Abdullah El Said deserves the Man of the Match award. Our target for every game is to win, so it's accepted to make some risk but not in an irrational way.
Milutin "Micho" Sredojevic (Head coach, Uganda)
It was a moment of experience that made the difference. I want to thank my players who gave their best and made their people proud. We came here to play three finals, we lost to Ghana by a penalty, lost to Egypt in the last minute and our ambition is to win against Mali and return home with pride.
At this level of competition, we have to be focused at the maximum level. I believe we were perfect on the tactical aspect, but we couldn't keep our concentration till the last moment. We played against a very good and talented team. We are coming back after 39-years and we are learning lessons and gaining experience but in a very hard way.